On Thursday morning, Ian visited the Vega Thurber lab at Oregon State University. The Vega Thurber lab works on viral (and bacterial) ecology of invertebrates, notably corals, so there is much synergy between our research groups. After breakfast, we talked about common problems associated with metavirome annotation, specifically the presence of many contaminants in reagents, which can cause problems for one-off metaviromes prepared without corresponding blanks. It’s a pervasive problem in the field of metagenomics. Despite huge efforts to clean reagents and make them DNA- or RNA-free, it is still quite possible to amplify rare viruses and bacteria from essentially nothing. This was first brought to light by Ian’s postdoc adviser, Jon Zehr, who noted that a huge number of heterotrophic nitrogenase sequences in the non-redundant database at GenBank were, in fact, easily amplified in blanks. Our group’s observations of both blank metaviromes (including those prepared with/without corresponding blank DNA extraction) and similarity of viruses seen across entire phyla (e.g. tunicates, crustaceans, echinoderms, and sharks) revealed that many parvoviruses, circoviruses, and even things like irido and herpesviruses aren’t really there. We’ve also tried to re-amplify many viral types that were apparently abundant in metaviromes from the source material, and couldn’t. So, the take home from our work is that it’s totally essential that blanks be included in metaviromic studies. We’re working on a database which includes all our known contaminants against which other researchers can BLAST their sequence data to identify spurious hits… stay tuned!
After meeting with the lab, Ian met with, and presented to, Bruce Menge’s lab, who investigate intertidal community ecology along the US West Coast. They’ve been investigating covariation between sea star wasting disease and oceanographic phenomena, including fine-resolution changes in pH and temperature over frequently-sampled time courses (in other words, lots of data and lots of work!). One thing that is definitely popping out of people’s observations are that there really are no universal physical or chemical phenomena that we’re measuring that explains the entire pattern of wasting disease occurrence or severity. But what is interesting is that there appears to be some pattern of which sea stars are most affected vs those that are not as badly affected. For more information, please contact Bruce or the MARINe websites.
Friday morning broke with Ian heading down to Newport and the Hatfield Marine Science Center to speak with Tim Miller-Morgan, chief vet at several aquariums on the coast, OSU faculty, and lead of Aquatic Animal Health at OR Sea Grant. Tim and Ian spoke about observations on the pathology and ecosystem level, and had a tour of the aquarium facilities. Future efforts there related to juvenile recruitment and temporal/longitudinal study of microbiome recruitment will provide insight into how the disease and its associated microorganisms change as animals develop. We also visited Rogue Brewery, which is where they’ve been brewing the Wasted Sea Star Purple Pale Ale. Unfortunately, Ian didn’t have a chance to meet up with the project coordinator, but did enjoy a fine lunch with Tim (Moco Loco – Ian’s indulgent favorite!).
So today up to Portland to meet up with old friends and then off to Seattle on Sunday to meet with the crew of the R/V Clifford Barnes (the vessel on which we have a January cruise scheduled), and Lesanna Lahner at the Seattle Aquarium. Ian will also have a chance to view stars – or what remain – at Mukilteo on Tuesday.
The experiments back in Ithaca appear to be going well, although no evidence of wasting in the inoculated stars yet. From previous experience this can take a bit of time. On return, we will look at whether we successfully transmitted SSaDV to the inoculated animals and make a decision then for more experiments. Stay tuned.
Sorry for no photos – hope to capture more imagery over the next few days!